RetrogeneDB - Retrocopy retro_ttru

                        
>retro_ttru_1171
TCATTATAATTTGGAGACAACAGATTGAGAAATGCACAAGCCACTATACAAGTTGCTCTGAATGTTCTTGAAACATGAGT

AACATGTTTGGAAAATGAACTCAGAGTGGCCTCTGAAAACTCTGGATTGTCAATATGTACAGTGAGTCTCCGGATTGATG

TTGGAATTTGACATGAAATTAAGAATAATGGAACAGCTCATTCTCTGGAACATATGAACTTCAATGTTACCAAAAAGAGA

TTCAGATTAGATCTGGAACTTGAAAATGAAAACATGGGTGCTCATTTCAACACCTATACCTCCAGAGAGCAGATCATGTA

TTATGCCAAAGAATTCTCTAAAGATTTGCCAAGAGCTGTACGCGTTCTTGCTGATATAACACAAAACAGTACATTGGCAG

AAGCAGAGACTGAGCACAAGTATAGAATAATCCTTAGAGAGATACACGAAATCAAAGCTAATTTACAAGAAGTTGTCTTT

TTATTATCTTAATGTCATAGTTTATCAAATACTGCACTTGGATTGACAATGTGGGGACCAACTGAAAATATCAAATCTAT

AAGTCATAAAGACTTAGTGGACTATATAACCACACATTATAAGAGGCCAAGAATAGTCCTTGCTATGGCTGGAGGAATCT

CCTATAGTGAACAGCTTAAGTTAACAAAGTTTCCTTTTGATGACTTTTTTTTTTTTTTTCCCACACACAAAGGAAAAAGA

ACAACTCTGGCTCCCTGCAAATTCACAGAAAGTGAGATTTGTTTGAGGAATGACAAGATGCCTTTGACACACCTTGCAAG

AGCTGTTCCAGCTGTTGGTTGGGAACATCCTGATACAATCTCTCTCATAGTTGCAAACACACTGACTGGCAACTAGGATT

GCCATTTCAGAGGAGGAATGAATTTAACTAGTAAGCCAGCCTGTCTCATCTGATGTGGCAACCTCTGCCATAGCTTCCAG

TCTTTCAACACTTGCTACACAGATACAGGATTGTGGGGACTCTATATGAGTTGTAAACCAGACATGGCTGCAGGCATGCT

ACATGTTGTTCAAAAAGAATACGTGTGACTCTGTATAAGTGTCACTGAAAGTAAAGTAGCACAAAATCTCTAGAAACAAA

ACATGTTTTTGCACTCTGAGTCAACTCCA

ORF - retro_ttru_1171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	67.87 %
Parental protein coverage:	84.21 %
Number of stop codons detected:	7
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalSLYFGGNRLRSTQAATQVVLNVPETHVTCLENGLRVASEDSGLSTCTVGLWIDAGSRYENEKNNGTAHFL
SL.FG.NRLR..QA..QV.LNV.ET.VTCLEN.LRVASE.SGLS.CTV.L.ID.G...E..KNNGTAH.L
RetrocopySL*FGDNRLRNAQATIQVALNVLET*VTCLENELRVASENSGLSICTVSLRIDVGI*HEI-KNNGTAHSL
ParentalEHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFSKDLPRAVEILADIIQNSTLGEAEIER
EHM.F..TKKR..LDLELE.ENMGAH.N.YTSREQ..YYAK.FSKDLPRAV..LADI.QNSTL.EAE.E.
RetrocopyEHMNFNVTKKRFRLDLELENENMGAHFNTYTSREQIMYYAKEFSKDLPRAVRVLADITQNSTLAEAETEH
ParentalERGVILREMQEVETNLQEVVF-DYLHATAYQ-NTALGRTILGPTENIKSINRKDLVDYITTHYKGPRIVL
....ILRE..E...NLQEVVF..YL....YQ.NTALG.T..GPTENIKSI..KDLVDYITTHYK.PRIVL
RetrocopyKYRIILREIHEIKANLQEVVF>YYLNVIVYQ<NTALGLTMWGPTENIKSISHKDLVDYITTHYKRPRIVL
ParentalAAAGGVSHDELLELAKFHFGD---SLSTHKGEIPALPPCKFTGSEIRVRDDKMPLAHLAIAVEAVGWAHP
A.AGG.S..E.L.L.KF.F.D......THKG....L.PCKFT.SEI..R.DKMPL.HLA.AV.AVGW.HP
RetrocopyAMAGGISYSEQLKLTKFPFDDXXXXXPTHKGKRTTLAPCKFTESEICLRNDKMPLTHLARAVPAVGWEHP
ParentalDTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCHGNLCHSFQSFNTSYTDTGLWGIYMVCEPATVGDML
DTI.L.VANTL.GN.D..F.GGMNL.SK.A.L...GNLCHSFQSFNT.YTDTGLWG.YM.C.P.....ML
RetrocopyDTISLIVANTLTGN*DCHFRGGMNLTSKPACLI*CGNLCHSFQSFNTCYTDTGLWGLYMSCKPDMAAGML
ParentalHVVQKEWMRLCTSVTESEVARAKNLLKTNMLLQLDGSTP
HVVQKE...LC.SVTES.V..A.NL.K.NM.L....STP
RetrocopyHVVQKEYV*LCISVTESKV--AQNL*KQNMFLHSE-STP

                            

                            Legend:
                            
                                *Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

                        

RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_1171 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1171 was not experimentally validated.

Retrocopy orthology:

Tursiops truncatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021200	1 retrocopy	retro_cjac_228,
Myotis lucifugus	ENSMLUG00000008798	1 retrocopy	retro_mluc_43,
Rattus norvegicus	ENSRNOG00000012693	1 retrocopy	retro_rnor_2963,
Tursiops truncatus	ENSTTRG00000010699	1 retrocopy	retro_ttru_1171 ,

	RetrogeneDB ID:	retro_ttru_1171
Retrocopy location	Organism:	*Dolphin (Tursiops truncatus)*
	Coordinates:	scaffold_106272:62623..63772(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PMPCB
	Ensembl ID:	ENSTTRG00000010699
	Aliases:	None
	Description:	peptidase (mitochondrial processing) beta [Source:HGNC Symbol;Acc:9119]

Parental	SLYFGGNRLRSTQAATQVVLNVPETHVTCLENGLRVASEDSGLSTCTVGLWIDAGSRYENEKNNGTAHFL
	SL.FG.NRLR..QA..QV.LNV.ET.VTCLEN.LRVASE.SGLS.CTV.L.ID.G...E..KNNGTAH.L
Retrocopy	SLFGDNRLRNAQATIQVALNVLETVTCLENELRVASENSGLSICTVSLRIDVGI*HEI-KNNGTAHSL

Parental	EHMAFKGTKKRSQLDLELEIENMGAHLNAYTSREQTVYYAKAFSKDLPRAVEILADIIQNSTLGEAEIER
	EHM.F..TKKR..LDLELE.ENMGAH.N.YTSREQ..YYAK.FSKDLPRAV..LADI.QNSTL.EAE.E.
Retrocopy	EHMNFNVTKKRFRLDLELENENMGAHFNTYTSREQIMYYAKEFSKDLPRAVRVLADITQNSTLAEAETEH

Parental	ERGVILREMQEVETNLQEVVF-DYLHATAYQ-NTALGRTILGPTENIKSINRKDLVDYITTHYKGPRIVL
	....ILRE..E...NLQEVVF..YL....YQ.NTALG.T..GPTENIKSI..KDLVDYITTHYK.PRIVL
Retrocopy	KYRIILREIHEIKANLQEVVF>YYLNVIVYQ<NTALGLTMWGPTENIKSISHKDLVDYITTHYKRPRIVL

Parental	AAAGGVSHDELLELAKFHFGD---SLSTHKGEIPALPPCKFTGSEIRVRDDKMPLAHLAIAVEAVGWAHP
	A.AGG.S..E.L.L.KF.F.D......THKG....L.PCKFT.SEI..R.DKMPL.HLA.AV.AVGW.HP
Retrocopy	AMAGGISYSEQLKLTKFPFDDXXXXXPTHKGKRTTLAPCKFTESEICLRNDKMPLTHLARAVPAVGWEHP

Parental	DTICLMVANTLIGNWDRSFGGGMNLSSKLAQLTCHGNLCHSFQSFNTSYTDTGLWGIYMVCEPATVGDML
	DTI.L.VANTL.GN.D..F.GGMNL.SK.A.L...GNLCHSFQSFNT.YTDTGLWG.YM.C.P.....ML
Retrocopy	DTISLIVANTLTGNDCHFRGGMNLTSKPACLICGNLCHSFQSFNTCYTDTGLWGLYMSCKPDMAAGML

Parental	HVVQKEWMRLCTSVTESEVARAKNLLKTNMLLQLDGSTP
	HVVQKE...LC.SVTES.V..A.NL.K.NM.L....STP
Retrocopy	HVVQKEYVLCISVTESKV--AQNLKQNMFLHSE-STP

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_ttru_1171